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- PDB-1koi: CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1koi
TitleCRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS COMPLEXED WITH NITRIC OXIDE AT 1.08 A RESOLUTION
ComponentsNITROPHORIN 4
KeywordsTRANSPORT PROTEIN / nitric oxide transport / ferric heme / anithistimine / lipocalin
Function / homology
Function and homology information


nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding
Similarity search - Function
Nitrophorin / Nitrophorin domain / Nitrophorin / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.08 Å
AuthorsRoberts, S.A. / Weichsel, A. / Qiu, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R.
CitationJournal: Biochemistry / Year: 2001
Title: Ligand-induced heme ruffling and bent no geometry in ultra-high-resolution structures of nitrophorin 4.
Authors: Roberts, S.A. / Weichsel, A. / Qiu, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R.
History
DepositionMay 3, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionJan 9, 2002ID: 1IKH
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NITROPHORIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9393
Polymers20,2931
Non-polymers6462
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.149, 42.419, 52.942
Angle α, β, γ (deg.)90.00, 94.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-299-

HOH

21A-378-

HOH

31A-437-

HOH

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Components

#1: Protein NITROPHORIN 4


Mass: 20292.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NITRIC OXIDE OCCUPIES THE SIXTH COORDINATION POSITION OF THE IRON. THE HEME IS DISORDERED BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS. THE ONLY EVIDENCE OF THIS DISORDER IS THE ...Details: NITRIC OXIDE OCCUPIES THE SIXTH COORDINATION POSITION OF THE IRON. THE HEME IS DISORDERED BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS. THE ONLY EVIDENCE OF THIS DISORDER IS THE APPEARANCE OF METHYL GROUPS CMB AND CMC AS VINYLS. THESE EXTRA ATOMS ARE CALLED CBBB AND CBCB.
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: PET-17B-NP4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q94734
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1→30 Å / Num. all: 83813 / Num. obs: 62726 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 4.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 38
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 15 / % possible all: 70

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementStarting model: pdb entry 1ERX

1erx


Resolution: 1.08→30 Å / Isotropic thermal model: All non-hydrogen atoms anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Shelx conjugate gradient refinement. Hydrogen atoms added at calculated positions. Heme and iron coordination sphere refined without restraints.
RfactorNum. reflectionSelection details
Rfree0.147 3144 random
Rwork0.115 --
all0.117 62726 -
obs0.115 59582 -
Displacement parametersBiso mean: 13 Å2
Refinement stepCycle: LAST / Resolution: 1.08→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 47 264 1763

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